[English] 日本語
Yorodumi
- PDB-7a23: Plant mitochondrial respiratory complex I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7a23
TitlePlant mitochondrial respiratory complex I
Components
  • 13kDa
  • 15kDa
  • 18kDa
  • 20.9kDa
  • 24kDa
  • 39kDa
  • 51kDa
  • 75kDa
  • ACPM1
  • ACPM2
  • AGGG
  • B12-1
  • B13
  • B14
  • B14.5a
  • B14.5b
  • B15
  • B16.6
  • B17.2
  • B18
  • B22
  • B8
  • B9
  • CA1
  • CAL1
  • ESSS
  • MWFE
  • Nad1m
  • Nad2m
  • Nad3m
  • Nad4Lm
  • Nad4m
  • Nad5m
  • Nad6m
  • Nad7m
  • Nad9m
  • P1
  • P2
  • PDSW
  • PGIV
  • PSST
  • TYKY
  • Unk1
  • Unk2
KeywordsMEMBRANE PROTEIN / Respiration / Complex I / mitochondria / plant
Function / homology
Function and homology information


respiratory chain complex I / cold acclimation / ubiquinone-6 biosynthetic process / Lyases; Carbon-oxygen lyases; Hydro-lyases / embryo development ending in seed dormancy / photorespiration / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / : / electron transport coupled proton transport ...respiratory chain complex I / cold acclimation / ubiquinone-6 biosynthetic process / Lyases; Carbon-oxygen lyases; Hydro-lyases / embryo development ending in seed dormancy / photorespiration / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / : / electron transport coupled proton transport / mitochondrial respiratory chain complex I / acyl binding / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / acyl carrier activity / ATP synthesis coupled electron transport / plastid / NADH dehydrogenase (ubiquinone) activity / ubiquinone binding / vacuolar membrane / vacuole / electron transport chain / cobalt ion binding / quinone binding / protein homotrimerization / response to osmotic stress / respiratory electron transport chain / respirasome / aerobic respiration / mitochondrial membrane / chloroplast / 2 iron, 2 sulfur cluster binding / mitochondrial intermembrane space / carbonate dehydratase activity / peroxisome / fatty acid biosynthetic process / NAD binding / 4 iron, 4 sulfur cluster binding / FMN binding / mitochondrial inner membrane / copper ion binding / response to oxidative stress / mitochondrial matrix / carbohydrate metabolic process / nucleolus / protein-containing complex binding / mitochondrion / zinc ion binding / integral component of membrane / extracellular region / plasma membrane / metal ion binding / nucleus / cytosol
Similarity search - Function
NADH-ubiquinone oxidoreductase 11 kDa subunit / NADH-ubiquinone oxidoreductase 11kDa subunit / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / NAD(P)H-binding / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NADH-ubiquinone oxidoreductase, subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 ...NADH-ubiquinone oxidoreductase 11 kDa subunit / NADH-ubiquinone oxidoreductase 11kDa subunit / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / NAD(P)H-binding / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NADH-ubiquinone oxidoreductase, subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH-ubiquinone oxidoreductase MWFE subunit / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / Zinc finger, CHCC-type / Zinc-finger domain / GRIM-19 protein / GRIM-19 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / 2Fe-2S iron-sulfur cluster binding domain / Thioredoxin-like [2Fe-2S] ferredoxin / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 5 C-terminus / NADH-quinone oxidoreductase, chain I / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-ubiquinone oxidoreductase B12 subunit family / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / : / NADH-quinone oxidoreductase, subunit D / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / NAD(P)-binding domain / ETC complex I subunit conserved region / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH-ubiquinone oxidoreductase subunit G, C-terminal / NADH-quinone oxidoreductase, chain G, C-terminal / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH ubiquinone oxidoreductase, F subunit / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH-plastoquinone oxidoreductase, chain 5 / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NuoE domain / NADH:ubiquinone oxidoreductase / NADH-ubiquinone oxidoreductase chain 4L/K / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / NADH dehydrogenase, subunit C / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH-quinone oxidoreductase subunit E, N-terminal / NADH-quinone oxidoreductase subunit E-like / Soluble ligand binding domain / SLBB domain / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH dehydrogenase / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / Proton-conducting membrane transporter / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region
Similarity search - Domain/homology
At1g67350 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial / Gamma carbonic anhydrase-like 1, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Gamma carbonic anhydrase 1, mitochondrial ...At1g67350 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial / Gamma carbonic anhydrase-like 1, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Gamma carbonic anhydrase 1, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-B, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-A / At2g46540/F11C10.23 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-B / Furry / AT2G31490 protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / Excitatory amino acid transporter / BICARBONATE ION / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A / Acyl carrier protein 2, mitochondrial / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / Chem-PEV / IRON/SULFUR CLUSTER / Phosphatidylinositol / UBIQUINONE-10 / CARDIOLIPIN / NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / Acyl carrier protein 1, mitochondrial / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 4L / At4g16450 / ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2 / Uncharacterized protein At2g27730, mitochondrial
Similarity search - Component
Biological speciesBrassica oleracea (wild cabbage)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsSoufari, H. / Waltz, F. / Hashem, Y.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-16-CE11-0024-02 France
European Research Council (ERC)759120
CitationJournal: Nat Commun / Year: 2020
Title: Specific features and assembly of the plant mitochondrial complex I revealed by cryo-EM.
Authors: Heddy Soufari / Camila Parrot / Lauriane Kuhn / Florent Waltz / Yaser Hashem /
Abstract: Mitochondria are the powerhouses of eukaryotic cells and the site of essential metabolic reactions. Complex I or NADH:ubiquinone oxidoreductase is the main entry site for electrons into the ...Mitochondria are the powerhouses of eukaryotic cells and the site of essential metabolic reactions. Complex I or NADH:ubiquinone oxidoreductase is the main entry site for electrons into the mitochondrial respiratory chain and constitutes the largest of the respiratory complexes. Its structure and composition vary across eukaryote species. However, high resolution structures are available only for one group of eukaryotes, opisthokonts. In plants, only biochemical studies were carried out, already hinting at the peculiar composition of complex I in the green lineage. Here, we report several cryo-electron microscopy structures of the plant mitochondrial complex I. We describe the structure and composition of the plant respiratory complex I, including the ancestral mitochondrial domain composed of the carbonic anhydrase. We show that the carbonic anhydrase is a heterotrimeric complex with only one conserved active site. This domain is crucial for the overall stability of complex I as well as a peculiar lipid complex composed of cardiolipin and phosphatidylinositols. Moreover, we also describe the structure of one of the plant-specific complex I assembly intermediates, lacking the whole P module, in presence of the maturation factor GLDH. GLDH prevents the binding of the plant specific P1 protein, responsible for the linkage of the P to the P module.
History
DepositionAug 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-11614
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 51kDa
I: Nad2m
J: Nad3m
N: Nad6m
H: Nad1m
K: Nad4Lm
Y: PGIV
Z: B16.6
V: MWFE
W: B9
S: B14.5a
i: B14.5b
j: 15kDa
G: Nad7m
C: 75kDa
T: 39kDa
F: Nad9m
B: 24kDa
O: 18kDa
P: 13kDa
R: B13
U: B17.2
E: PSST
D: TYKY
X: B14
c: 20.9kDa
Q: B8
k: ACPM1
r: Unk1
n: P2
o: CAL1
q: CA1
p: CA1
M: Nad4m
f: PDSW
g: ESSS
d: B22
a: Nad5m
b: B18
h: AGGG
e: ACPM2
l: B15
s: Unk2
m: P1
t: B12-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,005,12765
Polymers993,52245
Non-polymers11,60520
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

+
Protein , 42 types, 43 molecules AIJNHKYZVWSijGCTFBOPRUEDXcQkno...

#1: Protein 51kDa


Mass: 53522.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9FNN5*PLUS
#2: Protein Nad2m


Mass: 55486.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: O05000*PLUS
#3: Protein Nad3m


Mass: 13941.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: P92533*PLUS
#4: Protein Nad6m


Mass: 23700.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: P60497*PLUS
#5: Protein Nad1m


Mass: 36049.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: P92558*PLUS
#6: Protein Nad4Lm


Mass: 11139.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q04614*PLUS
#7: Protein PGIV


Mass: 11985.954 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q8LGE7*PLUS
#8: Protein B16.6


Mass: 16145.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q8RWA7*PLUS
#9: Protein MWFE


Mass: 7349.628 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9C9Z5*PLUS
#10: Protein B9


Mass: 6810.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9ZPY5*PLUS
#11: Protein B14.5a


Mass: 15060.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9SD78*PLUS
#12: Protein B14.5b


Mass: 9220.749 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q94AL6*PLUS
#13: Protein 15kDa


Mass: 9914.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9LZI6*PLUS
#14: Protein Nad7m


Mass: 45020.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: P93306*PLUS
#15: Protein 75kDa


Mass: 81619.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9FGI6*PLUS
#16: Protein 39kDa


Mass: 43988.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9SK66*PLUS
#17: Protein Nad9m


Mass: 22910.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q95748*PLUS
#18: Protein 24kDa


Mass: 28423.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: O22769*PLUS
#19: Protein 18kDa


Mass: 17160.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9FJW4*PLUS
#20: Protein 13kDa


Mass: 12251.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9M9M6*PLUS
#21: Protein B13


Mass: 19201.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9FLX7*PLUS
#22: Protein B17.2


Mass: 18346.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9M9M9*PLUS
#23: Protein PSST


Mass: 24071.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: P42027*PLUS
#24: Protein TYKY


Mass: 25410.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9FX83*PLUS
#25: Protein B14


Mass: 15102.261 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9LHI0*PLUS
#26: Protein 20.9kDa


Mass: 11355.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q84W12*PLUS
#27: Protein B8


Mass: 10865.765 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9FIJ2*PLUS
#28: Protein ACPM1


Mass: 13735.628 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: P53665*PLUS
#30: Protein P2


Mass: 11965.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9ZUX4*PLUS
#31: Protein CAL1


Mass: 27599.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9FMV1*PLUS
#32: Protein CA1


Mass: 30010.039 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9FWR5*PLUS
#33: Protein Nad4m


Mass: 55869.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: P93313*PLUS
#34: Protein PDSW


Mass: 12555.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9M9B4*PLUS
#35: Protein ESSS


Mass: 12680.462 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q8L3S7*PLUS
#36: Protein B22


Mass: 13638.335 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q945M1*PLUS
#37: Protein Nad5m


Mass: 74361.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: P29388*PLUS
#38: Protein B18


Mass: 11757.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9SKC9*PLUS
#39: Protein AGGG


Mass: 7582.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q8LDK3*PLUS
#40: Protein ACPM2


Mass: 14183.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: O80800*PLUS
#41: Protein B15


Mass: 8305.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9SIQ8*PLUS
#43: Protein P1


Mass: 11808.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9FYF8*PLUS
#44: Protein B12-1


Mass: 8239.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage) / References: UniProt: Q9M9R9*PLUS

-
Protein/peptide , 2 types, 2 molecules rs

#29: Protein/peptide Unk1


Mass: 1723.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage)
#42: Protein/peptide Unk2


Mass: 1439.571 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Brassica oleracea (wild cabbage)

-
Non-polymers , 10 types, 20 molecules

#45: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#46: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#47: Chemical ChemComp-T7X / Phosphatidylinositol / Phosphatidylinositol


Mass: 887.128 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C47H83O13P
#48: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#49: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C59H90O4
#50: Chemical ChemComp-PEV / (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLETHANOLAMINE / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Phosphatidylethanolamine


Mass: 720.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H78NO8P / Comment: POPE, phospholipid*YM
#51: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#52: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#53: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#54: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Mitochondrial respiratory complex I / Type: COMPLEX / Entity ID: #1-#44 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Brassica oleracea (wild cabbage) / Organ: Flower / Organelle: Mitochondria
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
13RELION3.0.83D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65018 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more